In The Age of Reason Paine states his views against all organized religion, not merely that which is enforced by the state. He was a deist himself. A deist, defined broadly, is one who accepts the existence of a Supreme Being, of God, without endorsing a specific or elaborated belief system claiming knowledge about God. Though some have defined deism as the belief that God created the world but from that point on did not interfere with it, Paine evidently regarded God as having an influence upon human affairs. Of God's role in his own life, he wrote that, when he escaped the guillotine during the Reign of Terror in Paris, he was "saved by Providence."
But the question of state-enforced religion is dealt with in The Age of Reason because, in Paine's view, it inevitably corrupts men by forcing them to pretend to accept things they don't believe in, and thus causes a general worsening of the human character and behavior. Paine's beliefs in this regard are a kind of subset of what all the English Dissenter sects believed. Paine came from a Quaker family. The Colonies were populated largely by Dissenters, those such as Puritans and Quakers who did not accept the Church of England and were being persecuted by the English ruling class, as well as other Protestant sects from elsewhere in Europe (such as Lutherans, Anabaptists, and Huguenots), Roman Catholics, and Jews.
In this mixture of faiths present in the New World, the entire idea of a state religion, as it existed in England, became obsolete. In the state governments set up after independence was declared in 1776, the men (such as Thomas Jefferson and John Adams) who drafted the constitutions of these states allowed for free religious expression for all citizens, regardless of their personal religious beliefs or non-beliefs.
Thomas Jefferson was a deist like his friend Paine, but was outwardly more reticent and less militant about the issue than Paine. The clearest evidence of the nature of Jefferson's religious beliefs is the so-called Jefferson Bible, a reduction of the New Testament Gospels to a purely naturalistic account of Jesus, omitting anything supernatural and excising all references to Jesus as a divinity. Jefferson can thus be described as a kind of secular Christian. But the most critical point about both Paine and Jefferson, and their input into the manner in which religion would be dealt with in the new country, is the principle that no one has the right to interfere with another's religious beliefs—or lack of them, for that matter. Both men recognized that a state religion causes people who dissent from it to behave hypocritically if they don't want to get persecuted, thrown in jail, or perhaps even killed.
Unfortunately, however, the absence of a religion enforced by the state does not mean persecution of religious minorities can't happen anyway. The exact thing has happened in the United States, first to the Irish Catholics who immigrated to America during the Famine of the 1840's, and subsequently to others such as the Jews. In the aftermath of 9/11 religious persecution began happening against Muslims and even others such as Sikhs, who were mistaken for Muslims. Persecution and harassment, at least until recently, very often have occurred on a local, individual level, such as kids in school being picked on for not being Christian. Hopefully, bullying measures in schools have reduced the occurrence of religious discrimination. Both Paine and Jefferson understood these harmful effects that religious belief and militantism can often have.